The electrophoretic properties of end-labeled DNA molecules in gels, polymer solutions and free-solutions: A theoretical and experimental study.

Abstract

Many aspects of the electrophoretic properties of end-labeled DNA molecules were studied in free-solutions, in dilute polymer solutions as well as in gels. New theoretical models for the friction coefficient of the hybrid molecules (for all three cases) are presented in this thesis. Our experimental investigation allowed us to validate the theoretical approach. A study of the gel edge electric field gradients in denaturing polyacrylamide gels was also performed and a method to take this gradient into account (in order to obtain reproducible and useful results) is presented. Using that method, the effect of steric trapping in polyacrylamide gels could be investigated (for different electric fields and polyacrylamide concentrations) and the validity of our biased reptation model was experimentally verified. Finally, we demonstrated theoretically that it is possible to build a ratchet system where two molecules having the same charge (DNA and end-labeled DNA fragments) can move in opposite directions when electrophoresed in a zero-integrated pulsed electric field.